10x single-cell introductory course, version 1

Course: https://www.tebteb.cc/blog/sc-series
Baseline: Ubuntu 24.04, R 4.3.3, Seurat 5.0.1.
See verification.txt for the actual run environment and limits.

Extract this archive into a new project directory, such as ~/sc-course.
Keep scripts/, configs/, results/ and logs/ within that directory.
The archive contains no expression matrix, FASTQ, or RDS objects.
The matrix is downloaded separately from 10x Genomics.

From the project directory:
  mkdir -p logs results
  Rscript scripts/00-check-env.R "$PWD"
  bash scripts/download-pbmc3k.sh "$PWD"
  Rscript scripts/01-import.R "$PWD"
  Rscript scripts/02-qc.R "$PWD"
  Rscript scripts/03-cluster.R "$PWD"
  Rscript scripts/04-markers.R "$PWD"

Inspect the marker plots and tables. Fill results/04-annotation.tsv.
Each row requires a cluster ID, cell_type and evidence.
Unknown is allowed with a reason; "pending review" must be replaced.
Then run:
  Rscript scripts/05-annotate.R "$PWD"

Scripts overwrite their stage outputs on rerun, except that 04-markers.R
preserves an existing manual annotation file. Back up reviewed results
before changing parameters. No script uploads user data.

The supplied demo annotation describes only the verified PBMC3k run.
Do not transfer cluster IDs to another dataset or a changed analysis.

Data source and attribution:
10x Genomics, 3k PBMCs from a Healthy Donor, Cell Ranger 1.1.0, CC BY 4.0.
https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0
File fingerprint recorded by this course (not a claimed publisher checksum):
847d6ebd9a1ec9a768f2be7e40ca42cbfe75ebeb6d76a4c24167041699dc28b5

Analysis method references: Seurat / SeuratObject official documentation.
https://satijalab.org/seurat/
These scripts implement a teaching workflow with auditable QC decisions
and manual evidence records; they do not introduce a new analysis method.
Complete Cell Ranger FASTQ processing was not run for this course edition.
